Taxonomic identification report

Sample ID: MP23-0431_matK

Department of Agriculture, Fisheries and Forestry logo

[analysis description + link to github repo]

Facility Hogwarts
Analyst John Doe
Analysis started 2025-05-03 01:28:15
Analysis completed 2025-05-03 01:28:15
Wall time 0:0:0 hours

Result overview

Inconclusive

Outcome: The analyst should attempt subjective species identification at the genus level.

Reasoning: [Flag 1C] >3 candidate species matched with high stringency (identity ≥ 98.5%).

Preliminary morphology ID confirmed? NA

Inconclusive taxonomic identity (Flag 1C) Planta.

Taxa of interest detected? True

Flag 2A: Taxon of interest detected in candidate species

Flag 5.1A: The given locus for this taxon is well represented in reference database (>5 entries)

Flag 5.2B: 10-90% of related taxa have reference sequence(s) at the given locus

Sample details

Locus matK
Preliminary ID Planta
Taxa of interest Nicotiana tabacum
Country Indonesia
Host NA
Sample ID MP23-0431_matK
Query DNA sequence

Analyst evaluation

Identification of candidate species

Flag 1C: The analyst should attempt subjective species identification at the genus level
>3 candidate species matched with high stringency (identity ≥ 98.5%)

Candidate hits must meet ONE of these criteria:

Minimum alignment length 400bp
Minimum query coverage 85.0%

Candidate hits have then been classified as follows:

Classification Alignment identity Number of hits Number of species
STRONG MATCH ≥ 98.5% 478 131
MODERATE MATCH ≥ 93.5% NA NA
NO MATCH < 93.5%

Candidate species

Species Hits Identity E-value Database coverage
Nicotiana glutinosa x Nicotiana tabacum 1 100.0% 0.0
Nicotiana tabacum 18 100.0% 0.0
Nicotiana sylvestris 2 100.0% 0.0
Nicotiana bonariensis 1 99.7% 0.0
Nicotiana attenuata 4 99.7% 0.0
Nicotiana x sanderae 1 99.7% 0.0
Nicotiana alata 2 99.7% 0.0
Nicotiana langsdorffii 1 99.7% 0.0
Nicotiana benthamiana 12 99.6% 0.0
Nicotiana goodspeedii 1 99.6% 0.0
Nicotiana forgetiana 1 99.6% 0.0
Nicotiana gossei 1 99.6% 0.0
Nicotiana plumbaginifolia 2 99.6% 0.0
Nicotiana umbratica 1 99.6% 0.0
Nicotiana longiflora 1 99.6% 0.0
Nicotiana occidentalis 1 99.6% 0.0
Nicotiana suaveolens 3 99.6% 0.0
Nicotiana simulans 1 99.6% 0.0
Nicotiana sp. 'rastroensis' 1 99.5% 0.0
Nicotiana exigua 2 99.5% 0.0
Nicotiana amplexicaulis 2 99.5% 0.0
Nicotiana repanda 2 99.5% 0.0
Nicotiana nesophila 1 99.5% 0.0
Nicotiana megalosiphon 2 99.5% 0.0
Nicotiana debneyi 2 99.5% 0.0
Nicotiana stocktonii 2 99.5% 0.0
Nicotiana rotundifolia 1 99.3% 0.0
Nicotiana glauca 8 99.3% 0.0
Nicotiana noctiflora 4 99.3% 0.0
Nicotiana linearis 1 99.3% 0.0
Nicotiana maritima 1 99.3% 0.0
Nicotiana nudicaulis 1 99.3% 0.0
Nicotiana miersii 2 99.3% 0.0
Nicotiana rosulata 1 99.3% 0.0
Nicotiana cavicola 1 99.2% 0.0
synthetic construct 1 99.2% 0.0
Nicotiana arentsii 1 99.2% 0.0
Nicotiana fragrans 1 99.2% 0.0
Nicotiana wigandioides 1 99.2% 0.0
Nicotiana undulata 2 99.2% 0.0
Nicotiana solanifolia 2 99.2% 0.0
Nicotiana petunioides 1 99.2% 0.0
Nicotiana corymbosa 1 99.0% 0.0
Nicotiana benavidesii 1 99.0% 0.0
Nicotiana glutinosa 1 99.0% 0.0
Nicotiana cordifolia 1 98.9% 0.0
Nicotiana raimondii 1 98.9% 0.0
Nicotiana otophora 3 98.9% 0.0
Trompettia cardenasiana 2 98.9% 0.0
Nicotiana thyrsiflora 1 98.9% 0.0
Nicotiana acaulis 1 98.9% 0.0
Nicotiana tomentosa 1 98.8% 0.0
Nicotiana tomentosiformis 2 98.8% 0.0
Lycium ferocissimum 219 98.6% 0.0
Lycium chinense 11 98.6% 0.0
Lycium barbarum 21 98.6% 0.0
Nicotiana quadrivalvis 1 98.6% 0.0
Nicotiana kawakamii 1 98.6% 0.0
Lycium dasystemum 5 98.6% 0.0
Eriolarynx australis 2 98.6% 0.0
Lycium yunnanense 1 98.6% 0.0
Iochroma ellipticum 1 98.6% 0.0
Anthocercis myosotidea 1 98.6% 0.0
Nicotiana trigonophylla 1 98.6% 0.0
Eriolarynx lorentzii 1 98.6% 0.0
Saracha punctata 3 98.6% 0.0
Salpichroa origanifolia 1 98.6% 0.0
Anthocercis angustifolia 1 98.6% 0.0
Lycium sp. 10 98.6% 0.0
Lycium pilifolium 1 98.6% 0.0
Vassobia dichotoma 2 98.6% 0.0
Nolana rostrata 1 98.6% 0.0
Lycium europaeum 1 98.6% 0.0
Nicotiana palmeri 1 98.6% 0.0
Anthotroche blackii 1 98.6% 0.0
Anthotroche pannosa 1 98.6% 0.0
Acnistus arborescens x Iochroma cyaneum 1 98.6% 0.0
Lycium hybrid cultivar 3 98.6% 0.0
Iochroma nitidum 1 98.6% 0.0
Eriolarynx fasciculata 1 98.6% 0.0
Lycium cinereum 1 98.6% 0.0
Iochroma salpoanum 1 98.6% 0.0
Lycium edgeworthii 1 98.6% 0.0
Lycium australe 1 98.6% 0.0
Dunalia brachyacantha 2 98.6% 0.0
Lycium ruthenicum 2 98.6% 0.0
Iochroma peruvianum 1 98.6% 0.0
Iochroma stenanthum 1 98.6% 0.0
Lycium mascarenense 1 98.6% 0.0
Iochroma loxense 1 98.6% 0.0
Lycium shawii 3 98.6% 0.0
Acnistus arborescens 2 98.6% 0.0
Nothocestrum latifolium 1 98.6% 0.0
Lycium cylindricum 3 98.6% 0.0
Lycium villosum 1 98.6% 0.0
Lycium truncatum 3 98.6% 0.0
Lycium schizocalyx 1 98.5% 0.0
Lycium carolinianum 1 98.5% 0.0
Lycium morongii 1 98.5% 0.0
Withania somnifera 1 98.5% 0.0
Nicotiana knightiana 3 98.5% 0.0
Brachistus nelsonii 1 98.5% 0.0
Iochroma lehmannii 2 98.5% 0.0
Cyphanthera microphylla 1 98.5% 0.0
Anthotroche walcottii 1 98.5% 0.0
Iochroma umbellatum 1 98.5% 0.0
Lycium prunus-spinosa 1 98.5% 0.0
Anthotroche myoporoides 1 98.5% 0.0
Lycium amarum 3 98.5% 0.0
Nicotiana clevelandii 1 98.5% 0.0
Datura inoxia 3 98.5% 0.0
Nicotiana obtusifolia 1 98.5% 0.0
Withania frutescens 2 98.5% 0.0
Iochroma tingoanum 1 98.5% 0.0
Cyphanthera albicans 1 98.5% 0.0
Datura stramonium 2 98.5% 0.0
Iochroma cyaneum 2 98.5% 0.0
Nicotiana paniculata 1 98.5% 0.0
Saracha nigribaccata 2 98.5% 0.0
Lycium elliotii 1 98.5% 0.0
Lycium schweinfurthii 1 98.5% 0.0
Anthocercis intricata 1 98.5% 0.0
Dunalia obovata 1 98.5% 0.0
Anthocercis sylvicola 1 98.5% 0.0
Leucophysalis grandiflora 1 98.5% 0.0
Nicotiana rustica 2 98.5% 0.0
Anthocercis viscosa 1 98.5% 0.0
Mandragora officinarum 1 98.5% 0.0
Nolana albescens 1 98.5% 0.0
Mandragora turcomanica 1 98.5% 0.0
Trozelia umbellata 1 98.5% 0.0

Boxplot of BLAST hit identity percent grouped by genus

The boxplot above shows the distribution of BLAST hits identity within each genus. Each data point shows the alignment identity between the query sequence and reference sequence. The analyst may wish to refer to this figure when making a subjective genus-level identification for the sample.

Analyst evaluation

Taxa of interest (TOI)

This sections shows the taxa of interest (TOI) specified by the sample submitter. Each of these taxa has been cross-referenced against the candidate species to determine if they might match the taxonomic identity of the sample. A blank row indicates a TOI that did not match any candidate species, meaning that it is unlikely that the sample matches that TOI.

Taxon of interest Match rank Match taxon Match species Match accession Match identity Database coverage
Nicotiana tabacum species Nicotiana tabacum Nicotiana tabacum AP019624 1.0

Reference sequence source diversity

This analysis evaluates how many independent sources have contributed to reference sequences for each candidate species. This provides a measure of confidence in the taxonomic annotation of references sequences. A sequence that has been annotated by multiple independent sources is more likely to have a correct taxonomic annotation.

Analyst evaluation

No candidate species to report on.

Intraspecies diversity

This section provides a phylogeny of the candidate reference sequences. The analyst can use this to make a subjective observation on how well the reference sequences are able to distinguish between species. If the phylogeny shows distinct clades for each species, we can be confident that the molecular data are capable of distinguishing between those species. However, if the phylogeny shows overlap between species, this reduces the capacity of the molecular data to confidently distinguish between those species. In some cases, we may see the query sequence falling outside of the adjacent species' clades, which indicates that our query species is not represented in the reference database, which could indicate a rare or novel species.

Analyst evaluation

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The phylogetic tree was constructed with FastME using the Neighbor-Joining method. Multiple-sequence alignment of the candidate reference sequences was performed using MAFFT. The visualization is rendered with TidyTree.

Taxonomy Check

The following resources can be used to ensure that the given taxonomy is legitimate and current.

Taxa Database
General GBIF
General ITIS
Mealybugs & scale ScaleNet database
Thrips Thripswiki
Spider Mites Spider Mites Database
Psocodea (Barklice, Booklice, and Parasitic Lice) Psocodea Species File Online
Orthoptera Orthoptera Species File Online
Drosophilidae TaxoDros
Diptera Catalog of the Diptera of the Australasian and Oceanian Regions
Systema Dipterorum
Aphids Aphid Species File
Ants AntWeb
AntCat
Lepidoptera (butterflies and moths) The Global Lepidoptera Names Index
Gracillariidae (primitive moths) Global Taxonomic Database of Gracillariidae
Pyralidae (pyralid moths) Global Information System on Pyraloidea
Tortricidae (tortrix moths) Tortricidae Resources on the Net